source/pymol/UNRESInpGen.py

   1 # -*- coding: utf-8 -*-
   2 '''
   3 -------------------------------------------------------------------------------
   4  UNRESInpGen.py - UNRES graphical input generator v 1.0
   5 -------------------------------------------------------------------------------
   6
   7  Written by Dawid Jagieła (lightnir@chem.univ.gda.pl)  Oct 2012
   8
   9 '''
  10
  11 from pymol import cmd,stored
  12 from Tkinter import *
  13 import tkFileDialog
  14 import tkMessageBox
  15 import Pmw
  16 import string
  17 import os
  18
  19 UNRESInpGen_version="1.0"
  20
  21 def __init__(self):
  22         self.UNRESInpGenWindow = None
  23         try:
  24                 self.menuBar.addcascademenu('Plugin', 'UNRESPlugins', 'UNRESPACK Plugins', label='UNRES Plugins')
  25         except:
  26                 pass
  27
  28         self.menuBar.addmenuitem('UNRESPlugins', 'command','UNRESInpGen',
  29                 label='UNRES Input Generator',
  30                 command = lambda s=self: createUNRESInpGen(s) )
  31
  32 def createUNRESInpGen(app):
  33         if (app.UNRESInpGenWindow == None):
  34                 app.UNRESInpGenWindow = UNRESInpGenerator(app)
  35         else:
  36                 app.UNRESInpGenWindow.myToggle()
  37
  38 #=================================================================
  39
  40
  41 class UNRESInpGenerator(Toplevel):
  42         global UNRESInpGen_version
  43         # Class variables
  44         """
  45         cv = IntVar()
  46         pp = IntVar()
  47         cp = IntVar()
  48         rv = IntVar()
  49         colorize = IntVar()
  50         """
  51         seq_letter = IntVar()
  52         writeSSbrige = IntVar()
  53         OM1Val = StringVar()
  54         OM2Val = StringVar()
  55         CART = IntVar()
  56         OVERLAP = IntVar()
  57         NOSEARCHSC = IntVar()
  58         objects_list = ['Select object']
  59         seq_list=[]
  60         seq_length=0
  61
  62         weights = ['WLONG','WSCC','WSCP','WELEC','WVDWPP','WEL_LOC','WCORR4','WCORR5','WCORR6','WTURN3','WTURN4','WTURN6','WSCCOR','WSTRAIN','WBOND','WTOR','WTORD','WANG','WSCLOC','SCAL14','SCALSCP','WCORRH','CUTOFF' ]
  63
  64         force_fields = [ {'FF':'GAB', 'WLONG' :'1.35279', 'WSCP'   :'1.59304', 'WELEC' :'0.71534', 'WBOND' :'1.00000', 'WANG'  :'1.13873', 'WSCLOC':'0.16258', 'WTOR':'1.98599', 'WTORD':'1.57069', 'WCORRH':'0.42887', 'WCORR5':'0.00000',
  65                                         'WCORR6':'0.00000', 'WEL_LOC':'0.16036', 'WTURN3':'1.68722', 'WTURN4':'0.66230', 'WTURN6':'0.00000', 'WVDWPP':'0.11371', 'WHPB':'1.00000', 'WCORR4':'0.00000', 'CUTOFF':'7.00000'},
  66                     {'FF':'E0G', 'WLONG':'1.70905', 'WSCP':'2.18310', 'WELEC':'1.06684', 'WBOND':'1.00000', 'WANG':'1.17536', 'WSCLOC':'0.22070', 'WTOR':'2.65798', 'WTORD':'2.00646', 'WCORRH':'0.23541', 'WCORR5':'0.00000',
  67                                         'WCORR6':'0.00000', 'WEL_LOC':'0.42789', 'WTURN3':'1.68126', 'WTURN4':'0.75080', 'WTURN6':'0.00000', 'WVDWPP':'0.27044', 'WHPB':'1.00000', 'WSCP14':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000'},
  68                     {'FF':'1L2Y_1LE1', 'WLONG' :'1.00000', 'WSCP'    :'1.23315', 'WELEC' : '0.84476', 'WBOND' :'1.00000', 'WANG'  :'0.62954', 'WSCLOC': '0.10554', 'WTOR': '1.84316', 'WTORD' : '1.26571', 'WCORRH': '0.19212', 'WCORR5': '0.00000',
  69                                         'WCORR6':'0.00000', 'WEL_LOC':'0.37357', 'WTURN3':'1.40323', 'WTURN4':'0.64673', 'WTURN6':'0.00000', 'WVDWPP': '0.23173', 'WHPB': '1.00000', 'WSCCOR': '0.00000', 'CUTOFF': '7.00000', 'WCORR4': '0.00000'},
  70                     {'FF':'4P',  'WSC':'1.00000', 'WSCP':'2.73684', 'WELEC':'0.06833', 'WANG':'4.15526', 'WSCLOC':'0.16761', 'WTOR':'2.99546', 'WTORD':'2.89720', 'WCORRH':'1.98989', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.60072',
  71                                         'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  72                     {'FF':'3P',  'WSC':'1.00000', 'WSCP':'2.85111', 'WELEC':'0.36281', 'WANG':'3.95152', 'WSCLOC':'0.15244', 'WTOR':'3.00008', 'WTORD':'2.89863', 'WCORRH':'1.91423', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.72128',
  73                                         'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  74                         {'FF':'CASP5',          'WSC':'1.00000',        'WSCP':'1.54864', 'WELEC':'0.20016', 'WANG': '1.00572', 'WSCLOC': '0.06764', 'WTOR':'1.70537', 'WTORD':'1.24442', 'WCORRH':'0.91583', 'WCORR5':'0.00607', 'WCORR6':'0.02316', 'WEL_LOC':'1.51083',
  75                                         'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
  76                         {'FF':'ALPHABETA',      'WSC':'1.00000', 'WSCP':'1.43178', 'WELEC':'0.41501', 'WANG':'0.37790', 'WSCLOC':'0.12880', 'WTOR':'1.98784', 'WCORRH':'2.50526', 'WCORR5':'0.23873', 'WCORR6':'0.76327', 'WEL_LOC':'2.97687', 'WTURN3':'0.09261',
  77                                         'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  78                         {'FF':'BETA', 'WSC':'1.00000', 'WSCP':'1.10684', 'WELEC':'0.70000', 'WANG':'0.80775', 'WSCLOC':'1.91939', 'WTOR':'3.36070', 'WCORRH':'2.50000', 'WCORR5':'0.99949', 'WCORR6':'0.46247', 'WEL_LOC':'2.50000', 'WTURN3':'1.80121',
  79                                         'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  80                         {'FF':'ALPHA', 'WSC':'1.00000', 'WSCP':'0.72364', 'WELEC':'1.10890', 'WANG':'0.68702', 'WSCLOC':'1.79888', 'WTOR':'0.30562', 'WCORRH':'1.09616', 'WCORR5':'0.17452', 'WCORR6':'0.36878', 'WEL_LOC':'0.19508', 'WTURN3':'0.00000',
  81                                         'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
  82                         {'FF':'CASP3', 'WELEC':'1.50000', 'WSTRAIN':'1.00000', 'WTOR':'0.08617', 'WANG':'0.10384', 'WSCLOC':'0.10384', 'WCORR':'1.50000', 'WTURN3':'0.00000', 'WTURN4':'0.00000', 'WTURN6':'0.00000', 'WEL_LOC':'0.00000', 'WCORR5':'0.00000',
  83                                         'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
  84         ]
  85
  86         one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', 'GLY':'G', 'PRO':'P', 'CYS':'C'}
  87
  88
  89         def __init__(self,parent):
  90                 # Create the GUI window
  91                 root = Toplevel.__init__(self)
  92                 self.config(width=400, height=300)              # create a root window
  93                 self.title("UNRES Input Generator v"+UNRESInpGen_version)                 # Set window title
  94                 self.resizable(0, 0)                                # Disable window resize
  95                 self.geometry('-40+40')                             # Set window placement
  96
  97                 # Create the Balloon.
  98                 self.balloon = Pmw.Balloon(root)
  99
 100                 #================================
 101                 # "Main Options" group
 102                 #
 103                 self.gr1 = Pmw.Group(self,tag_text = 'Main options')
 104                 self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 105
 106                 # - Create title Entryfield & Label
 107                 #self.l1 = Label(self.gr1.interior(), text="Title:")
 108                 #self.l1.grid(row=0, column=0,sticky=E)
 109                 self.e1 = Pmw.EntryField(self.gr1.interior(),
 110                         labelpos='w',
 111                         label_text="Title:",
 112                         validate = {'max': 80 },
 113                 #       value ="(Place input information here)"
 114                 )
 115                 self.e1.component('entry').config(width=80)
 116                 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
 117
 118                 # - Create "choose method" OptionMenu
 119                 self.OM1Val.set('MD')
 120                 self.optmenu1 =  Pmw.OptionMenu(self.gr1.interior(),
 121                         labelpos = 'w',
 122                         label_text = 'Choose method:',
 123                         menubutton_textvariable = self.OM1Val,
 124                         items = ['MD', 'MREMD', 'MINIMIZE' ],
 125                         command = self.switch_options,
 126                         menubutton_width = 10
 127                 )
 128                 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
 129
 130
 131                 # - Seed entryfield
 132                 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
 133                         labelpos='w',
 134                         label_text="Seed",
 135                         validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
 136                         value = "-1111333"
 137                 )
 138                 self.gr1.e1.component('entry').config(width=8)
 139                 self.gr1.e1.grid(row=1, column=2, sticky=W)
 140
 141                 #==================================
 142                 # - MD options frame
 143                 #
 144                 self.gr1.md = Frame(self.gr1.interior())
 145                 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
 146
 147                 # -- nstep entryfield
 148                 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
 149                         labelpos='w',
 150                         label_text="NSTEP",
 151                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 152                         value = "500000"
 153                 )
 154                 self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
 155                 self.gr1.md.e1.component('entry').config(width=8)
 156                 self.gr1.md.e1.grid(row=0, column=0, sticky=E)
 157
 158                 # -- ntwe entryfield
 159                 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
 160                         labelpos='w',
 161                         label_text="NTWE",
 162                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 163                         value = "100"
 164                 )
 165                 self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
 166                 self.gr1.md.e2.component('entry').config(width=8)
 167                 self.gr1.md.e2.grid(row=0,column=1, sticky=E)
 168
 169                 # -- ntwx entryfield
 170                 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
 171                         labelpos='w',
 172                         label_text="NTWX",
 173                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 174                         value = "1000"
 175                 )
 176                 self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
 177                 self.gr1.md.e3.component('entry').config(width=8)
 178                 self.gr1.md.e3.grid(row=0,column=2, sticky=E)
 179
 180                 # -- dt entryfield
 181                 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
 182                         labelpos='w',
 183                         label_text="DT",
 184                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 185                         value = "0.1")
 186                 self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
 187                 self.gr1.md.e4.component('entry').config(width=8)
 188                 self.gr1.md.e4.grid(row=0,column=3, sticky=E)
 189
 190                 # -- damax entryfield
 191                 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
 192                         labelpos='w',
 193                         label_text="DAMAX",
 194                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 195                         value = "1.0")
 196                 self.balloon.bind(self.gr1.md.e5, "Maximum allowed change of acceleration during a single time step.\nThe time step gets scaled down, if this is exceeded.")
 197                 self.gr1.md.e5.component('entry').config(width=8)
 198                 self.gr1.md.e5.grid(row=1,column=0, sticky=E)
 199
 200                 # -- dvmax entryfield
 201                 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
 202                         labelpos='w',
 203                         label_text="DVMAX",
 204                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 205                         value = "20.0")
 206                 self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
 207                 self.gr1.md.e6.component('entry').config(width=8)
 208                 self.gr1.md.e6.grid(row=1,column=1, sticky=E)
 209
 210                 # -- restet_vel entryfield
 211                 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
 212                         labelpos='w',
 213                         label_text="RESET_VEL",
 214                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
 215                         value = "1000")
 216                 self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
 217                 self.gr1.md.e7.component('entry').config(width=8)
 218                 self.gr1.md.e7.grid(row=1,column=2, sticky=E)
 219
 220
 221                 #=================================
 222                 #  - thermostat frame
 223                 #
 224                 self.gr1.th = Frame(self.gr1.interior())
 225                 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
 226
 227                 # -- Thermostat optionmenu
 228                 self.gr1.th.optmenu1 =  Pmw.OptionMenu(self.gr1.th,
 229                         labelpos = 'w',
 230                         label_text = 'thermostat',
 231                         items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
 232                         command=self.set_thermostat,
 233                         menubutton_width = 15
 234                 )
 235                 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
 236
 237                 # -- t_bath entryfield
 238                 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
 239                         labelpos='w',
 240                         label_text="T_BATH",
 241                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
 242                         value = "300.0")
 243                 self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
 244                 self.gr1.th.e1.component('entry').config(width=8)
 245                 self.gr1.th.e1.pack(side=LEFT)
 246
 247                 # -- tau_bath entryfield
 248                 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
 249                         labelpos='w',
 250                         label_text="TAU_BATH",
 251                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 252                         value = "1.0")
 253                 self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
 254                 self.gr1.th.e2.component('entry').config(width=8)
 255                 self.gr1.th.e2.pack(side=LEFT)
 256
 257                 # -- q_np entryfield
 258                 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
 259                         labelpos='w',
 260                         label_text="Q_NP",
 261                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 262                         value = "0.1")
 263                 self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
 264                 self.gr1.th.e3.component('entry').config(width=8)
 265                 #self.gr1.th.e2.pack(side=LEFT)
 266
 267
 268                 #=================================
 269                 # - Minimization frame
 270                 self.gr1.mi = Frame(self.gr1.interior())
 271                 #self.gr1.mi.grid(row=4, column=0, columnspan=5,sticky=W+E)
 272
 273                 self.gr1.mi.e1 = Pmw.EntryField(self.gr1.mi,
 274                         labelpos='w',
 275                         label_text="MAXMIN",
 276                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 277                         value = "2000" )
 278                 self.balloon.bind(self.gr1.mi.e1,'Maximum number of iterations of the SUMSL minimizer.')
 279                 self.gr1.mi.e1.component('entry').config(width=8)
 280                 self.gr1.mi.e1.pack(side=LEFT)
 281
 282                 self.gr1.mi.e2 = Pmw.EntryField(self.gr1.mi,
 283                         labelpos='w',
 284                         label_text="MAXFUN",
 285                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 286                         value = "5000" )
 287                 self.balloon.bind(self.gr1.mi.e2,'Maximum number of function evaluations in a single minimization.')
 288                 self.gr1.mi.e2.component('entry').config(width=8)
 289                 self.gr1.mi.e2.pack(side=LEFT)
 290
 291                 self.gr1.mi.c1 = Checkbutton(self.gr1.mi,
 292                         text = "CART",
 293                         variable = self.CART )
 294                 self.balloon.bind(self.gr1.mi.c1,'Minimize in virtual-bond vectors instead of angles.')
 295                 self.gr1.mi.c1.pack(side=LEFT)
 296
 297                 self.gr1.mi.c2 = Checkbutton(self.gr1.mi,
 298                         text = "OVERLAP",
 299                         variable = self.OVERLAP )
 300                 self.balloon.bind(self.gr1.mi.c2,'Fix overlaping sidechains.')
 301                 self.gr1.mi.c2.pack(side=LEFT)
 302
 303                 self.gr1.mi.c3 = Checkbutton(self.gr1.mi,
 304                         text = "NOSEARCHSC",
 305                         variable = self.NOSEARCHSC )
 306                 #self.balloon.bind(self.gr1.mi.c3,'Minimize in virtual-bond vectors instead of angles.')
 307                 self.gr1.mi.c3.pack(side=LEFT)
 308
 309
 310
 311                 #=================================
 312                 # "Force field options" group
 313                 #
 314                 self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
 315                 self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 316
 317                 # - Create "force field parameters" Option menu
 318                 self.OM2Val.set('Custom')
 319                 self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
 320                 label_text = 'Force field parameters:',
 321                         labelpos = 'w',
 322                         menubutton_textvariable = self.OM2Val,
 323                         items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
 324                         initialitem = 'Custom',
 325                         menubutton_width = 10,
 326                         command=self.set_force_field
 327                 )
 328                 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
 329
 330                 # Force field parameters Entry Fields
 331                 self.ef = []
 332                 for i in range(0,len(self.weights)):
 333                         self.ef.append(Pmw.EntryField(self.gr2.interior(),
 334                         labelpos='n',
 335                         label_text=self.weights[i],
 336                         validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
 337                         value = '1.00000'))
 338                         self.ef[i].component('entry').config(width=8)
 339                         self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
 340                 # "Sequence" group
 341                 self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
 342                 self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 343
 344                 self.gr3.f1 = Frame(self.gr3.interior())
 345                 # Object List
 346                 self.cb2 = Pmw.ComboBox(self.gr3.f1,
 347                         labelpos = 'w',
 348                         #entry_relief = 'raised',
 349                         label_text = 'Selection/Object',
 350                         scrolledlist_items = self.objects_list
 351                 )
 352                 self.cb2.pack(side=LEFT)
 353                 # refresh button
 354                 self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
 355                 self.gr3.btn1.pack(side=LEFT)
 356                 # Get sequence button
 357                 self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
 358                 self.gr3.btn2.pack(side=LEFT)
 359
 360                 self.gr3.f1.pack(expand="yes",fill="both")
 361
 362                 # Disulfide brige checkbox
 363                 self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
 364                 self.gr3.chk.pack(side=LEFT)
 365
 366                 # Sequence text
 367                 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
 368                         columnheader = 1,
 369                         columnheader_width = 3,
 370                         rowheader = 1,
 371                         rowheader_width = 4,
 372                         usehullsize=1,
 373                         hull_width=30,
 374                         hull_height=180,
 375                         text_padx = 4,
 376                         text_pady = 4,
 377                         Header_padx = 4,
 378                         rowheader_pady = 4,
 379                 )
 380                 # Sequence text - create the header line
 381                 headerline = ''
 382                 for column in range(1,21):
 383                         headerline = headerline + ('%-4s' % str(column) )
 384                 self.gr3.t1.component('columnheader').insert('0.0',headerline)
 385
 386                 self.gr3.t1.pack(expand="yes",fill="both")
 387
 388                 # Add some buttons
 389                 btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
 390                 btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
 391                 btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
 392                 btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
 393
 394                 # create callback to prevent window kill
 395                 self.protocol("WM_DELETE_WINDOW", self.myHide)
 396
 397         def ToggleColor(self):
 398                 if self.colorize.get()==1:
 399                         for i in range(0,len(self.res_states)):
 400                                 UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
 401                 else:
 402                         for i in range(0,len(self.res_states)):
 403                                 UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
 404
 405         def myShow(self):
 406                 self.deiconify()
 407
 408         def myHide(self):
 409                 self.withdraw()
 410
 411         def myToggle(self):
 412                 if self.state() == "normal":
 413                         self.myHide()
 414                 elif self.state() == "withdrawn":
 415                         self.myShow()
 416
 417         def get_selections(self):
 418                 self.objects_list = []
 419                 for item in cmd.get_names("all"):
 420                         if cmd.get_type(item)=="object:molecule":
 421                                 self.objects_list.append(item)
 422                         if cmd.get_type(item)=="selection":
 423                                 if item[0]<>"_":
 424                                         self.objects_list.append(item)
 425
 426         def get_nonstandard(self):
 427                 stored.list=[]
 428                 cmd.iterate("(all)","stored.list.append(resn)")
 429                 stored.list=list(Set(stored.list))  # remove duplicates
 430                 # Remove standard amino acids and water from list
 431                 for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
 432                         try:
 433                                 stored.list.remove(m)
 434                         except ValueError:
 435                                 pass
 436                 UNRESInpGenWindow.cbcr1.setlist(stored.list)
 437
 438         def refresh_list(self):
 439                 # Save old values
 440                 old = self.objects_list
 441                 try:
 442                         old_cb2=self.cb2.getvalue()[0]
 443                 except:
 444                         old_cb2=''
 445                 self.get_selections()
 446
 447                 # Update selectionlist if needed
 448                 if not(old==self.objects_list):
 449                         self.cb2.setlist(self.objects_list)
 450                         self.cb2.setlist(self.objects_list)
 451
 452                 if not(old_cb2 in self.objects_list):
 453                         # No - clear the combobox entry
 454                         self.cb2.component('entryfield').clear()
 455                 else:
 456                         # Yes - set the old value
 457                         self.cb2.selectitem(old_cb2,setentry=1)
 458
 459
 460         def get_seq(self):
 461                 # Get the number of chains
 462                 try:
 463                         nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 464                 except:
 465                         nchains=0
 466                 pass
 467
 468                 if (nchains>0):
 469                         self.seq_list=[]
 470                 offset=0
 471                 seq_data=''
 472                 self.seq_length=0
 473                 for chain in range(0,nchains):
 474                         # Get only amonoacids, N-terminus acyl and C-terminus amide
 475                         # example:      (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
 476                         # No chain information or only one chain
 477                         if nchains==1:
 478                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 479                         # Chain information is present
 480                         else:
 481                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & chain "+cmd.get_chains(self.cb2.getvalue()[0])[chain]+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 482                         # dodaj separator lancuchow
 483                         if chain>0:
 484                                 self.seq_list.append("D  ")
 485                                 self.seq_length+=1
 486
 487
 488                         # Zamiana chronionych
 489                         # ACE ALA ALA NH2 D   ACE ALA ALA NH2
 490                         # GLY ALA ALA GLY D   GLY ALA ALA GLY
 491                         # Zamiana niechronionych
 492                         #     ALA ALA     D       ALA ALA
 493                         # D   ALA ALA     D       ALA ALA D
 494                         #
 495                         # j - licznik pozycji reszty
 496                         j=0
 497                         for i in atomchain:
 498                                 self.seq_length+=1
 499                                 if str(i.resn)=="NH2":
 500                                         self.seq_list.append("GLY")
 501                                 elif str(i.resn)=="NHH":
 502                                         self.seq_list.append("GLY")
 503                                 elif str(i.resn)=="NME":
 504                                         self.seq_list.append("GLY")
 505                                 elif str(i.resn)=="ACE":
 506                                         self.seq_list.append("GLY")
 507                                 elif str(i.resn)=="GLY":
 508                                         self.seq_list.append("GLY")
 509                                 else:
 510                                         if j==0 and chain==0:
 511                                                 self.seq_list.append("D  ")
 512                                                 self.seq_list.append(str(i.resn))
 513                                                 self.seq_length+=1
 514                                         elif j==len(atomchain)-1 and chain==(nchains-1):
 515                                                 self.seq_list.append(str(i.resn))
 516                                                 self.seq_list.append("D  ")
 517                                                 self.seq_length+=1
 518                                         else:
 519                                                 self.seq_list.append(str(i.resn))
 520                                 j+=1
 521                 rows=0
 522                 #row_header='0'  - old header
 523                 row_header='1'
 524                 # tag setup
 525                 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
 526                 tagList=[]
 527                 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
 528                 CysTagList=[]
 529
 530                 for i in range(len(self.seq_list)):
 531                         # Dummy tag
 532                         if self.seq_list[i]=="D  ":
 533                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 534                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 535                                 tagList.append(tag1)
 536                                 tagList.append(tag2)
 537                         # Cysteine tag
 538                         if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
 539                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 540                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 541                                 CysTagList.append(tag1)
 542                                 CysTagList.append(tag2)
 543                         #
 544                         offset+=1
 545                         seq_data=seq_data+self.seq_list[i]+" "
 546                         # Line Wrap
 547                         if offset>19:
 548                                 offset=0
 549                                 seq_data=seq_data+'\n'
 550                                 rows+=1
 551                                 #row_header=row_header+'\n'+str(rows*20)    - old header
 552                                 row_header=row_header+'\n'+str(rows+1)
 553
 554                 self.gr3.t1.clear()
 555                 self.gr3.t1.insert('end',seq_data)
 556                 # Apply tags
 557                 if len(tagList):
 558                         apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
 559                 if len(CysTagList):
 560                         apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
 561
 562                 # Show row header
 563                 self.gr3.t1.component('rowheader').delete(1.0, END)
 564                 self.gr3.t1.component('rowheader').insert('end',row_header)
 565
 566
 567         def switch_options(self,calctype):
 568                 '''
 569                         Displays the options available to set depending on the currently
 570                         selected calculation type
 571                 '''
 572                 # Hide all
 573                 self.gr1.th.grid_remove()
 574                 self.gr1.md.grid_remove()
 575                 self.gr1.mi.grid_remove()
 576                 # Show MD stuff
 577                 if  self.OM1Val.get()=="MD":
 578                         self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
 579                         self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
 580                 elif self.OM1Val.get()=="MINIMIZE":
 581                         self.gr1.mi.grid(row=4,column=0,columnspan=5, sticky=W+E)
 582
 583
 584         def set_force_field(self, pole):
 585                 '''
 586                         Enables/disables entryfields for force field perameters depending
 587                         on the currently selected force field
 588                 '''
 589                 for ff in self.force_fields:
 590                         if ff['FF']==pole:
 591                                 #print ff
 592                                 for i in range(0,len(self.weights)):
 593                                         if ff.has_key(self.weights[i]):
 594                                                 self.ef[i].setvalue(ff.get(self.weights[i]))
 595                                                 self.ef[i].component('entry').config(state=NORMAL)
 596                                         else:
 597                                                 self.ef[i].component('entry').config(state=DISABLED)
 598                         # Custom force field
 599                         elif pole=='Custom':
 600                                 for i in range(0,len(self.weights)):
 601                                         self.ef[i].component('entry').config(state=NORMAL)
 602
 603         def set_thermostat(self,thermostat):
 604                 '''
 605                         Display additional widget acording to selected thermostat
 606                 '''
 607                 #print thermostat
 608                 self.gr1.th.e2.pack_forget()
 609                 self.gr1.th.e3.pack_forget()
 610                 if thermostat=='Berendsen':
 611                         self.gr1.th.e2.pack(side=LEFT)
 612                 elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
 613                         self.gr1.th.e3.pack(side=LEFT)
 614
 615         def fortran_format(self,s):
 616                 '''
 617                     Formats string containing keywords to wrap over 80 columns
 618                 '''
 619                 tmpstr=''
 620                 column=1
 621                 for k in s.split():
 622                         if column+len(k)+1<80:
 623                                 tmpstr+=k+' '
 624                                 column+=len(k)+1
 625                         else:
 626                                 tmpstr+=" "*(80-column)+"&\n"+k+" "
 627                                 column=len(k)+2
 628                 tmpstr+='\n'
 629                 return tmpstr
 630
 631         def get_weights(self):
 632                 '''
 633                         Get the force field weights
 634                 '''
 635                 s = ''
 636                 for i in range(0,len(self.weights)):
 637                         if self.ef[i].component('entry').cget("state")=="normal":
 638                                 s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
 639                 return s
 640
 641         def get_md_opt(self):
 642                 s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
 643                 s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
 644                 s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
 645                 s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
 646
 647                 # Thermostat options
 648                 term=self.gr1.th.optmenu1.getvalue()
 649                 #print term
 650                 if term=="Berendsen":
 651                         s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
 652                 elif term=="Nose-Poincare 1999":
 653                         s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
 654                 elif term=="Nose-Poincare 2001":
 655                         s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
 656                 elif term=="Nose-Hoover":
 657                         s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
 658                 elif term=="Langevin":
 659                         s+="LANG=1 "
 660
 661                 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
 662                 return s
 663
 664         def get_minim_opt(self):
 665                 s = "MAXMIN="+self.gr1.mi.e1.getvalue()+" MAXFUN="+self.gr1.mi.e2.getvalue()
 666                 return s
 667
 668
 669         def get_seq_data(self):
 670                 '''
 671                         Dumps the sequence and disulfide bridge information
 672                 '''
 673                 # write sequence length
 674                 s = str(self.seq_length)+"\n"
 675                 #
 676                 #try:
 677                 #       nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 678                 #except:
 679                 #       nchains=0
 680                 #pass
 681
 682                 chains=cmd.get_chains(self.cb2.getvalue()[0])
 683                 nchains=len(chains)
 684                 #print "chains  : ",chains
 685                 #print "nchains : ",nchains
 686
 687                 # apply one space before each sequence line
 688                 seq=self.gr3.t1.get()
 689                 for line in seq.split('\n'):
 690                         s+=" "+line+"\n"
 691                 # remove last newline character
 692                 s = s[:-1]
 693
 694                 # disulfide bridges - get half-cysteines by selection:
 695         # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
 696                 ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
 697                 nSSbr=len(ncys)/2
 698
 699
 700                 # Is "Write disulfide brige" checked?
 701                 # yes
 702                 if self.writeSSbrige.get():
 703                         # write number of half-cysteines
 704                         s+=str(len(ncys))+"\n"
 705                         if len(ncys)==0:
 706                                 # No half-cysteines, cys position = 0
 707                                 s+=" 0\n"
 708                         else:
 709                                 # Write half-cysteine positions in sequence
 710                                 #
 711                                 # get first chain
 712                                 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
 713
 714                                 # calculate base offset in first chain (if dummy atom present offset = 1 )
 715                                 if first.atom[0].resn=="GLY":
 716                                         boff=0
 717                                 else:
 718                                         boff=1
 719
 720                                 # create dictionary of PDB chain/resi to UNRES_index
 721                                 unresidx={}
 722                                 for c in ncys:
 723                                         # calculate residue index offset from first residue in chain containing half-cysteine
 724                                         fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
 725                                         roff=int(c.resi)-int(fresinchain[0].resi)+1
 726
 727                                         resb=0
 728                                         coff=0
 729                                         for r in chains:
 730                                                 if c.chain==r:
 731                                                         break
 732                                                 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
 733                                                 coff+=1
 734                                         # add key/value to dictionary
 735                                         unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
 736                                         s+=" "+str(boff+resb+coff+roff)
 737                                 s+="\n"
 738
 739                                 # Write the number of disulfide bridges
 740                                 s+=" "+str(nSSbr)+"\n"
 741
 742                                 lista_mostkow=[]
 743                                 for c in ncys:
 744                                         # get neibhoring Sulfur atom
 745                                         opis=c.chain+str(c.resi)
 746                                         lista_mostkow.append(opis)
 747                                         nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
 748                                         opis2=nbr.chain+str(nbr.resi)
 749                                         if opis2 not in lista_mostkow:
 750                                                 # Write witch half-cysteines build the i-th disulfide bridge
 751                                                 s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
 752                                                 #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
 753                 # Don't writeSSbrige
 754                 else:
 755                         s+="0\n 0\n"
 756
 757
 758                 return s
 759
 760
 761         def write_cshell(self, cshname,prefix):
 762                 '''
 763                         Writes the C-shell script needed to run UNRES calculations
 764                 '''
 765                 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
 766
 767                 # number of processors per energy
 768                 if self.OM1Val.get()=="MD":
 769                         s+='setenv FGPROCS 1\n'
 770
 771                 # Potential
 772                 if self.OM2Val.get()=="CASP3":
 773                         s+='setenv POT LJ\n'
 774                 else:
 775                         s+='setenv POT GB\n'
 776
 777                 # input file
 778                 s+='setenv PREFIX '+prefix+'\n'
 779
 780                 # Parallel stuff
 781                 s+='setenv OUT1FILE YES\n'
 782
 783                 # force filed parameters
 784                 s+='#---------------------------------------------------------------------\n'
 785                 s+='setenv DD $UNRES_ROOT/PARAM\n'
 786
 787                 if self.OM2Val.get()=="CASP3":
 788                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 789                         s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
 790                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
 791                         s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 792                 elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
 793                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 794                         s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 795                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 796                 elif self.OM2Val.get()=="CASP5":
 797                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 798                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 799                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_iter7n_c\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 800                 elif self.OM2Val.get()=="3P":
 801                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 802                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\n'
 803                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 804                 elif self.OM2Val.get()=="4P":
 805                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 806                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
 807                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 808                 elif self.OM2Val.get()=="GAB":
 809                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 810                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k\n'
 811                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 812                 elif self.OM2Val.get()=="E0G":
 813                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 814                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc\n'
 815                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 816                 elif self.OM2Val.get()=="1L2Y_1LE1":
 817                         s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
 818                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
 819                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 820                 elif self.OM2Val.get()=="Custom":
 821                         s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
 822                         s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
 823                         s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
 824
 825
 826
 827                 s+='setenv PATTERN $DD/patterns.cart\n'
 828                 s+='#---------------------------------------------------------------------\n'
 829                 s+='$UNRES_BIN $*\n'
 830
 831                 f = open(cshname, 'w')
 832                 f.write(s)
 833                 f.close()
 834
 835
 836         def setenv_info(self):
 837                 print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
 838                   UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
 839                   UNRES_BIN  - the UNRES binary you want to execute
 840                 '''
 841
 842
 843         def ok(self):
 844                 '''
 845                     Writes the actual input
 846                 '''
 847                 myFormats = [
 848                     ('Input files','*.inp'),
 849                         ('All files','*.*')
 850                 ]
 851                 # Write error handling for empty sequence
 852                 #
 853                 s=self.gr3.t1.getvalue()
 854                 if len(s.strip())==0:
 855                         tkMessageBox.showerror("NEED SEQUENCE DATA!", "NEED SEQUENCE DATA!\n\nYou have not loaded the sequence information. Please click \"Refresh\", choose an object from the list and click \"Get sequence\".")
 856                 else:
 857                         # Display dialog window
 858                         fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
 859                         if fout:
 860                                 print "Saving input file %s" % fout.name
 861                                 # Get input header
 862                                 text2save=self.fortran_format(self.e1.get())
 863                                 # Get main options
 864                                 mainopt="SEED="+self.gr1.e1.get()+" "
 865                                 if self.OM1Val.get()=="MD":
 866                                         mainopt+="MD PDBREF EXTCONF"
 867                                 elif self.OM1Val.get()=="MREMD":
 868                                         mainopt+="RE "
 869                                 elif self.OM1Val.get()=="MINIMIZE":
 870                                         mainopt+="PDBREF MINIMIZE RESCALE_MODE=0"
 871                                         if self.CART.get():
 872                                                 mainopt+=" CART"
 873                                         if self.OVERLAP.get():
 874                                                 mainopt+=" OVERLAP"
 875                                         if self.NOSEARCHSC.get():
 876                                                 mainopt+=" NOSERARCHSC"
 877                                 text2save+=self.fortran_format(mainopt)
 878                                 # Get aux options
 879
 880                                 if self.OM1Val.get()=="MD":
 881                                         text2save+=self.fortran_format(self.get_md_opt())
 882                                 elif self.OM1Val.get()=="MINIMIZE":
 883                                         text2save+=self.fortran_format(self.get_minim_opt())
 884
 885                                 # Get force fields parameters
 886                                 text2save+=self.fortran_format(self.get_weights())
 887
 888                                 # PDB reference
 889                                 pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
 890                                 text2save+=pdbreffn+"\n"
 891                                 print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
 892                                 cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
 893
 894                                 # C-shell script
 895                                 cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
 896                                 print "Writing C-shell script %s" % (cshellfn)
 897                                 prefix=os.path.basename(os.path.splitext(fout.name)[0])
 898                                 self.write_cshell(cshellfn,prefix)
 899
 900                                 # Get sequence data
 901                                 text2save+=self.get_seq_data()
 902
 903                                 fout.write(text2save)
 904                                 fout.close()
 905
 906                                 # ENV Varaiables info
 907                                 self.setenv_info()